Extracts the completed data from a mids object

Takes an object of class mids, fills in the missing data, and returns the completed data in a specified format.

Usage

# S3 method for class 'mids'
complete(
  data,
  action = 1L,
  include = FALSE,
  mild = FALSE,
  order = c("last", "first"),
  ...
)

Arguments

data: An object of class mids as created by the function mice().
action: A numeric vector or a keyword. Numeric values between 1 and data$m return the data with imputation number action filled in. The value of action = 0 return the original data, with missing values. action can also be one of the following keywords: "all", "long", "broad" and "repeated". See the Details section for the interpretation. The default is action = 1L returns the first imputed data set.
include: A logical to indicate whether the original data with the missing values should be included.
mild: A logical indicating whether the return value should always be an object of class mild. Setting mild = TRUE overrides action keywords "long", "broad" and "repeated". The default is FALSE.
order: Either "first" or "last". Only relevant when action == "long". Writes the ".imp" and ".id" in columns 1 and 2. The default is order = "last". Included for backward compatibility with "< mice 3.16.0".
...: Additional arguments. Not used.

Value

Complete data set with missing values replaced by imputations. A data.frame, or a list of data frames of class mild.

Details

The argument action can be length-1 character, which is matched to one of the following keywords:

"all": produces a mild object of imputed data sets. When include = TRUE, then the original data are appended as the first list element;
"long": produces a data set where imputed data sets are stacked vertically. The columns are added: 1) .imp, integer, referring the imputation number, and 2) .id, character, the row names of data$data;
"stacked": same as "long" but without the two additional columns;
"broad": produces a data set with where imputed data sets are stacked horizontally. Columns are ordered as in the original data. The imputation number is appended to each column name;
"repeated": same as "broad", but with columns in a different order.

Note

Technical note: mice 3.7.5 renamed the complete() function to complete.mids() and exported it as an S3 method of the generic tidyr::complete(). Name clashes between mice::complete() and tidyr::complete() should no longer occur.

Examples


# obtain first imputed data set
sum(is.na(nhanes2))
#> [1] 27
imp <- mice(nhanes2, print = FALSE, maxit = 1)
dat <- complete(imp)
sum(is.na(dat))
#> [1] 0

# obtain stacked third and fifth imputation
dat <- complete(imp, c(3, 5))

# obtain all datasets, with additional identifiers
head(complete(imp, "long"))
#>     age  bmi hyp chl .imp .id
#> 1 20-39 29.6  no 199    1   1
#> 2 40-59 22.7  no 187    1   2
#> 3 20-39 29.6  no 187    1   3
#> 4 60-99 21.7 yes 204    1   4
#> 5 20-39 20.4  no 113    1   5
#> 6 60-99 22.7 yes 184    1   6

# same, but now as list, mild object
dslist <- complete(imp, "all")
length(dslist)
#> [1] 5

# same, but also include the original data
dslist <- complete(imp, "all", include = TRUE)
length(dslist)
#> [1] 6

# select original + 3 + 5, store as mild
dslist <- complete(imp, c(0, 3, 5), mild = TRUE)
names(dslist)
#> [1] "0" "3" "5"

Extracts the completed data from a `mids` object